Biology

09 November 2017: the eighth great ape and the problem with ‘species’

Until recently, only seven species made up the group of primates known as the great apes, or Hominidae. Two orangutan species (Sumatran and Bornean), two gorilla species (eastern and western), two chimpanzee species (chimpanzees and bonobos), and us.

But in a report recently published in Current Biology, an international team of scientists announced a new hominid with fewer than 800 members, Pongo tapanuliensis, found just south of Lake Toba in Sumatra. To save your tongue twisting around that particular binomen, we can call it the Tapanuli orangutan.

The scientists compared skull, jaw and dental characteristics of a Tapanuli specimen with those of the Sumatran and Bornean species, and analysed 37 orangutan genomes as a second line of evidence.

Orangutan

Three species of orangutan: from left, Bornean, Sumatran, Tapanuli. Photo credits: Eric Kilby, Aiwok, Tim Laman

The report gained a great deal of media attention: not only because we humans had a new cousin, but because the Tapanuli is an endangered species.

However, there were dissenting voices. In an interview with the ABC, for example, Lee Christidis from Southern Cross University pointed out that the analysis had been carried out on only one specimen and that the DNA evidence was at best ambiguous.

It’s only fair to point out that it’s often the case that a species will be described by a single representative organism, or, as happens frequently in palaeontology, those fragments of a single organism that have been fossilised or otherwise survived over many millions of years.

The report also generated discussion about what we mean by the word ‘species’. Jerry Coyne, professor emeritus at the University of Chicago and author of the excellent Why Evolution is True, wrote in his blog:

‘Not only do I see this new “species” as merely an isolated and genetically differentiated population (as are many human populations regarded as H. sapiens), but I’d also contend that there is only one species of orangutan overall, with these three groups all being subspecies. Sadly, a lot of systematists don’t see it that way, as they seem to think that any isolated population, if it can be told apart morphologically or genetically from others, warrants being named as a new species. Yet to evolutionists, a “species” is not an arbitrary segment of nature’s continuum, but real entities that maintain their “realness” because they don’t exchange any (or many) genes with other such entities where they cohabit in nature.’

But is this indeed the definition of species with the greatest currency among most biologists?

To start with, there has to a definition that works across all fields. A primatologist cannot have a different concept of species from, say, an entomologist, or the whole point of taxonomy – the orderly classification of living things that demonstrates their evolutionary relationships – starts to fall apart.

This doesn’t mean that definitions in biology – or any scientific endeavour, for that matter – are written in stone. As our knowledge of the world around us grows, the language we use to explore, explicate and explain that knowledge must also grow.

The definition I was taught at school is not dissimilar to Coyne’s quoted above, and is based on what is called the Biological Species Concept (BSC), developed by Ernst Mayr and Theodosius Dobzhansky in the early 1960s (Coyne did some graduate work under Dobzhansky at Rockefeller University). As Colin Groves, professor emeritus at the Australian National University, wrote, ‘This concept states that under natural conditions a species ‘should not exchange genes with other species’[i]. Groves goes on to point out that ‘ … the popular idea that two species are “unable” to interbreed is  a misunderstanding: it is not that they cannot interbreed, it is that they do not.‘

The BSC was further refined by Mayr and Jared Diamond in a paper on Melanesian birds in 2001, and then in 2004 by the aforementioned Jerry Coyne with H. Allen Orr in a book about speciation called, appropriately enough, Speciation.

Groves argues that the modified definition of BSC risks different standards of comparison in different taxonomic groups: it’s a definition that won’t work across different fields, in other words.

Groves again: ‘If a genus contains a pair of sympatric[ii] sibling species (species that differ only slightly, inconspicuously), the standard for species recognition will be set much “lower” than in a genus in which sympatric species pairs are grossly different. It is the search for objective standards – for an operational means of distinguishing species – that has been responsible for the controversies that marked taxonomic discussions over the past 15 or 20 years.’[iii]Taxonomy

Many biologists now use what is called the Phylogenetic Species Concept (PSC), developed by American biologist Joel Cracraft from the early 1980s. Put very simply, in this concept a species is the smallest population of organisms that is measurably different from other populations sharing the same ancestry. Note that this concept says nothing whatsoever about species sharing genes, such as happened between Homo sapiens and H. neanderthalensis around 100,000 years ago.

It’s important to note that both the BSC and the PSC are attempts to operationalise the evolutionary concept of species; that is, that a species is an evolutionary lineage.

While the report in Current Biology describing the Tapanuli orangutan as a new species of great ape has, for the most part, been received positively, the fact that many distinguished scientists question the findings shows that the debate about what constitutes a species is ongoing.

[i] Groves, Colin. ‘Speciation in hominin evolution’; African Genesis: Perspectives on Hominin Evolution; ed Reynolds, Sally C. & Gallagher, Andrew; Cambridge University Press; Cambridge; 2012, p 46.

[ii] Sympatry occurs when two or more species live in the same geographic area.

[iii] Ibid.

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17 October 2017: Walking statues, colonialism and free speech

I am a white male living in a society largely designed by white males for the benefit of white males. As such, I am a member of history’s most privileged group, a group that numbers no more than a few hundred million in a world inhabited by over seven billion human beings.

What got me here, together with every other member of that group, was a toxic mixture of imperialism and colonialism. Not toxic for me, I hasten to point out, but toxic for billions of other human beings.

It’s not necessary to point out how many first peoples suffered because of European expansion from the 15th through to the 20th centuries. Nor should we defend that expansion by referring to the benefits brought by the introduction of ‘Western’ inventions such as double-entry bookkeeping and modern farming methods, as if they were handed out by the Conquistadors and Australia’s first settlers at the same time as the distribution of smallpox and musket balls.Imperialism

Imperialism and colonialism also transformed slavery into a global business. The fact that Europeans didn’t invent slavery shouldn’t stop us acknowledging that developments such as double-entry bookkeeping helped Europeans perfect it, in the same way the musket ball helped perfect total war.

In a very roundabout way that brings me to the topic of walking statues. Specifically, Rapa Nui’s moai – the monumental statues of Easter Island.

Rapa Nui has been used as the example par excellence of ‘ecocide’, what happens to a society that selfishly exploits its own environment beyond recovery and thereby destroys itself. I swallowed without questioning this explanation for the island’s depopulation and deforestation, promoted in books like Jared Diamond’s Collapse: How Societies Choose to Fail or Survive.

But it may not be true.

University of Bristol researcher Catrine Jarman explains in her article in The Conversation, that many decades of archaeological research on Rapa Nui ‘paints a very different picture’.

As Jarman writes:

‘The ecocide hypothesis centres on two major claims. First, that the island’s population was reduced from several tens of thousands in its heyday, to a diminutive 1,500-3,000 when Europeans first arrived in the early 18th century.

‘Second, that the palm trees that once covered the island were callously cut down by the Rapa Nui population to move statues. With no trees to anchor the soil, fertile land eroded away resulting in poor crop yields, while a lack of wood meant islanders couldn’t build canoes to access fish or move statues. This led to internecine warfare and, ultimately, cannibalism.’

Essentially, there is no convincing evidence that Rapa Nui’s population declined before first European contact in 1722. Furthermore, recent evidence suggests that the island’s population successfully sustained itself for centuries despite deforestation occurring soon after the island’s initial settlement by humans, deforestation caused by the accidental introduction of the Polynesian rat which ate palm nuts and saplings.

So what did happen to the people of Rapa Nui?

Again, in Jarman’s own words:

‘Throughout the 19th century, South American slave raids took away as much as half of the native population. By 1877, the Rapanui numbered just 111. Introduced disease, destruction of property and enforced migration by European traders further decimated the natives and lead to increased conflict among those remaining.’

The disaster that befell the people of Rapa Nui came about because of the slave trade of the 18th and 19th centuries, itself a result of European imperialism and colonialism. Effectively, the victims of that depopulation subsequently were found guilty of the crime.

If the forests weren’t cut down to move the moai, how did the islanders transport the statues from where they were made to where they were eventually sited?

Moai

Rapa Nui moai

It turns out they probably moved them in the same way you or I would move a heavy washing machine or refrigerator … they walked them. Admittedly, this involved a great deal more human muscle power and coordination than two people clumsily angling white goods through a narrow corridor. Recent experiments show that this was perfectly possible.

(For a full explanation of how this was done, and the true story of how Rapa Nui became depopulated, check out The Statues that Walked, by Terry Hunt and Carl Lipo.)

I can’t argue that imperialism and colonialism had no benefits. It benefitted me, for example. Without them I wouldn’t be here now, a middle-aged male living in middle-class splendour in Australia, a collection of ex-colonies. Nor can I argue against the proposal that the modern world is a direct result of those movements. Nor can I argue against the proposal that industrialisation and modernisation, two direct products of those movements, hasn’t improved the lot of billions of human beings over the last two centuries.

What I can’t argue, however, is what Portland State University’s Bruce Gilley suggests in an article recently published in Third World Quarterly. An associate professor of political science, Gilley proposes that ex-colonies that develop their Western colonial legacy do better that those that reject that legacy. One of the examples he uses is the modern nation of Singapore.

I suspect Gilley is wrong, especially in the case of Singapore where its success is almost entirely due to the self-created ‘Singapore model’, a mixture of democracy, authoritarianism and meritocracy that has delivered remarkable growth and one of the world’s highest standards of living. But I strongly believe Gilley has every right to express his academic opinion in an academic journal.

Singapore

Singapore skyline

As reported by Andy Ngo in Quillette, both Gilley and the journal’s editor-in-chief Shahid Qadir received threats of violence after the appearance of the article on 8 September, and the publishers of Third World Quarterly have withdrawn it. I recommend reading Ngo’s piece to get the full story.

I do not think hate speech or speech inciting violence should ever be published, whether it is an article written for a journal, an opinion piece in a newspaper, or an enraged Tweet by an American president. But I do not think it is right to censure someone’s research because you disagree with its conclusion. In fact, that kind of thinking encourages hate speech and incites violence. Worse, ultimately, it shuts off debate, dialogue and intellectual curiosity.

The problem for those who think that the evils of colonialism are so great that any defence of it is anathema and should be closed down is simply this: it allows history to be written by those who shout the loudest. It establishes a precedent, a precedent that may one day lead to the censorship of articles that explain why colonialism was wrong, and how the moai of Rapa Nui came to walk.

(NB Jared Diamond has responded to some of the claims made in Hunt and Lipo’s book, The Statues that Walked. You can check that out here. Thanks to friend, physicist and fellow-writer Rob Porteous for the heads-up.)

07 October 2017: New evidence suggest we are much older than 300,000 years

In a recent blog I wrote about new dates for skulls found in the cave of Jebel Irhoud in Morocco in the 1960s. Originally assessed as belonging to Homo neanderthalensis (an assessment that was soon challenged), a reappraisal published in Nature this year confirmed they were in fact H. sapiens skulls; the great surprise was that the reappraisal determined them to be at least 300,000 years old.

Jebel Irhoud

Cast of Jebel Irhoud 1 from the Australian National University. Photo: Simon Brown

New work done by scientists in Sweden and South Africa, and reported in Science, have now dated DNA obtained from a 2000-year-old Khoe-San skeleton apparently unmixed with Bantu or Eurasian DNA, as having separated from other H. sapiens sometime between 260,000 and 350,000 years ago.

The San are the First People of South Africa, Botswana and Namibia. Indeed, they may be the First People, the ancestral group all modern humans are descended from, or at the very least very closely related to them.

The San are the most genetically diverse of all humans living today. In an episode of Catalyst on the ABC about her research on San DNA, Professor Vanessa Hayes said, ‘There’s more similarity between myself and a Han Chinese than between two San people.’

Bushman

San hunter/gatherer

As reported in Science, the recent work on San DNA involved several ancient individuals, but the standout dates were given by DNA from the genome of a hunter-gatherer boy known as Ballito Bay A. The scientists concluded that, ‘ … our results show that the deepest split among modern humans (the estimated latest time for the emergence of H. sapiens) occurred at between 350 kya and 260 kya.’

Given that the skulls found in Morocco have been dated to at least 300,000 years ago, it would seem not unreasonable to consider the older dates for the emergence of H. sapiens – 350,000 years ago – being closer to the mark than the lower date of 260,000 years ago.

This new evidence also adds weight to the theory that our species may have partly evolved in South Africa.

In the last eight months, we have seen conservative estimates for the age of our species jump from 190,000 years old to almost double that. It’s been an extraordinary year for palaeoanthropology.

22 May 2016: Crows got smarts

Corvus_corax_tibetanus

Corvus corax, the common raven. Photo: Pkspks [CC BY-SA 4.0]

It’s no secret that corvids – crows and ravens – are exceptionally smart for birds, especially at problem solving. Now an experiment carried out with ravens provides evidence they may have a basic Theory of Mind as well; this means they have an ability to attribute mental states they experience to another raven.

In a paper published in Nature in February, researchers Thomas Bugnyar, Stephan Reber and Cameron Buckner from the universities of Vienna and Houston, carried out an ingenious experiment that tested how ravens caching food behaved when they thought they were being seen by another raven.

There is increasing evidence that the Theory of Mind exists in chimpanzees, bonobos, scrub jays and ravens. How equivalent the experience of a ToM is between species is, so far, untestable, but the strong possibility that some form of ToM exists in different animals provides yet more evidence of the complexity of the mental life of species apart from humans.

Not only does this add weight to calls that humans should reconsider the way they relate to other animals, especially the often appalling way we treat farmed and domesticated animals, but firmly places Homo sapiens as the product of the same evolutionary process that produced ravens, dogs and garden slugs.

16 May 2016: New dates for the ‘Hobbit’

Homo floresiensis

Photo: Ryan Somma

Updating my blog celebrating the 10th anniversary of the discovery of Homo floresiensis, better known as the ‘Hobbit’, a letter in Nature has revised the most recent dates for the remains from 12,000 years back to 60,000 years. The sediment layers in the cave of Liang Bua on the Indonesian island of Flores, where the remains were discovered, had not been laid evenly, leading to an initial miscalculation.

Stone artefacts attributed to H. floresiensis are dated more recently, to 50,000 years ago.

The biggest implication of the new dates is that it is now less likely that the ‘Hobbit’ coexisted at the same time as H. sapiens on Flores. Although it cannot be ruled out, the earliest dates for human occupation at Flores is 50,000 years, leaving a very narrow window of opportunity.

11 February 2016: Digging for relatives

DSC02344

Elen Feuerriegel with thermoplastic copy of H. naledi lower jaw.

“Sometimes I can’t believe it happened,” said Elen Feuerriegel as the 3D printer by her side chugs out a thermoplastic copy of the cranium of an ancient human.

“I’m doing something ordinary, something I do every day, and then remember that two years ago I was working 30 metres underground recovering the remains of Homo naledi, a previously unknown human species.”

Feuerriegel, a PhD student in palaeoanthropology at the Australian National University, was one of six excavators – dubbed underground astronauts by an excited media – who retrieved the bones of up to 15 individuals from a small and almost inaccessible cave.

Part of an expedition organised by Professor Lee Berger from the University of Witwatersrand to investigate the Rising Star Cave in South Africa, it was the task of the Feuerriegel and the other five excavators to reach a small and unmapped annex to the cave system called the Dinaledi Chamber.

“To get to the chamber meant worming our way through a fissure that in one place narrowed to just 18 centimetres,” Feuerriegel said. “The fissure itself was a 12-metre drop that ended in a tiny landing, followed by another four metre drop to the floor of the chamber.”

What Feuerriegel first saw there will stay with her for the rest of her life.

“It was a wonderful, exhilarating experience. It was incredible amount of fossil material in one place. It was almost impossible to move without stepping on a jaw or leg bone.

“As our eyes got used to the dimness and we became more experienced at discerning fossils in the floor sediment, new finds seemed to appear out of nowhere.”

Despite her interest in science starting as a young teenager, her appearance at the Rising Star Cave System was never a given. She reached palaeoanthropology through a route almost as torturous as the entrance to the Dinaledi Chamber.

“My first love was marine biology, particularly sharks. That somehow morphed into a fascination with volcanoes. Then my mum, an information architect, helped me put together a web page for a school project I did on human evolution.”

Feuerriegel speaks about evolution through natural selection with a focused passion.

“For me, evolution is the great leveler. We humans are as subject to evolutionary forces as other species.”

The American crime procedural CSI: Crime Scene Investigation also stirred in her an interest in anatomy.

She did her first degree in sociocultural anthropology at the University of Queensland. “I’d given up on the idea of palaeoanthropology until I did an intensive summer course on human evolution.”

With an honours degree in her pocket, Feuerriegel came to the ANU to do her masters, and in 2013 began her PhD in palaeoanthropology.

Later that year, Lee Berger put the call out for people with a special and unusual skill set.

“He wanted skinny palaeoanthropologists who were also experienced climbers or cavers.”

Feuerriegel, who enjoyed wall-climbing and hiking, and had previously worked in a mine shaft in Sima de las Palomas in Spain looking for the remains of Neanderthals, applied for one of the openings.

Underground astronauts

The Underground Astronauts: Becca Peixotto, Alia Gurtov, Elen Feuerriegel, Marina Elliott, K. Lindsay Hunter, Hannah Morris. Photo: John Hawks

“Despite the specialist skill set, there were 60 applicants. I was one of six chosen.”

Within three weeks of an online interview, Feuerriegel found herself in South Africa retrieving the remains of a new human species, Homo naledi.

“We worked in two shifts, each with three excavators and two support cavers. Each shift lasted anywhere between three and six hours, depending on the task. The expedition tried to get at least two shifts down in the chamber every day, and sometimes three.

“For the first few days it could take up to an hour to get down from the surface to the chamber, but by the end of our stay there we’d reduced that to 20 minutes, giving us much more time for the real work.”

Towards the end of the work, seasonal rains raised the water table.

“There was no danger to us – the site was well above the water table – but conditions gradually got worse and surfaces more and more slippery.”

In the end, the excavators recovered the remains of 15 individuals, male and female, ranging in age from neonatal to an older female with very worn teeth.

Feuerriegel said she’s sure what the team discovered is a new species of ancient human.

“Morphologically, Homo naledi sits somewhere in the bridge between the latter Australopithecines and the early Homo, having features of both as well as some unique features all of its own. Exactly where it fits is something we don’t know yet.

“The other thing we don’t know at this point is how old the remains are. The bones we found had not yet been replaced with minerals like silica, but were still made up of hydroxylapatite, a form of calcium.”

She said if the remains proved to be between two and three million years old, H. naledi is the earliest definite example of Homo with skeletal material representing the whole body.

“If the remains are between one and two million years old, the date’s about right for a hominin of H.  naledi’s morphology.

“And if the date is less than one million years old, it means we have multiple species of hominins existing at the same time in South Africa. In that case, H. naledi’s small braincase and primitive morphology must make us seriously reconsider what it means to be a member of our own genus.”

Early reaction among some palaeoanthropologists hasn’t been all positive.

“Claims that the remains represent an early form of Homo erectus are fanciful,” Feuerriegel said. “A lot of critics have also focused on Lee’s description of the appearance of the bodies in one place as ‘ritual’.

“In this case, we aren’t suggesting anything spiritual, only that it represents repeated and deliberate behaviour.”

One of the career highlight for any palaeoanthropologist is to be one of the official ‘describers’ of a new species; thanks to her time in South Africa, Feuerriegel, at the age of 26 and still at least six months from finishing her PhD, is one of the names on the scientific paper officially naming the new species.

“I’ll also be lead author on a paper describing H. naledi’s upper limb, an area of morphology I’m particularly interested in.”

Feuerriegel said humans hold themselves on a pedestal as a species, above and apart from our ancestors.

“If there’s one thing H. naledi illustrates, it’s that the characteristics and behaviours we believe make us unique are not so unique after all.”

04 September 2015: Neither one thing nor the other

P. myojinensis

P. myojinensis. The blue structure is the nucleus, the red structures the endosymbionts.

A remarkable creature discovered in the ocean southeast of Japan – that doesn’t quite seem to belong to any of the three known domains – may provide evidence of how complex multicellular life evolved on Earth.

In 2010, a scientific expedition to the Myojin Knoll, about 35 kilometres southeast of the Japanese island of Aogashima, collected biological samples from a hydrothermal vent more than 1,200 metres below the surface.

The samples were frozen and then embedded in epoxy resin; the resin was then prepared for study by being sliced into ultrathin sections.

That’s when the researchers discovered they had collected one truly remarkable specimen, a single-celled organism that lays somewhere between prokaryotes, organisms like bacteria and archaea, and eukaryotes, the basis of complex organisms such as fungi, plants and … well … us.

The main differences between prokaryotes and eukaryotes are that the former do not have a nucleus surrounded by a membrane, or any membrane-bound organelles such as mitochondria or chloroplasts.

As described in the journal Microscopy, the cell, dubbed Parakaryon myojinensis, was discovered on one of the bristles of a type of Polychaete called a scale worm. It was 10 micrometres long and three wide, much larger than most bacteria. Inside the cell the researchers discovered a nucleus with a membrane. As well, they discovered three endosymbionts, organisms that live symbiotically inside another, also surrounded by membranes. Obviously, then, the cell was not a prokaryote.

However, the nucleus of P. myojinensis was surrounded by a single membrane and consisted of DNA fibres, whereas a nucleus in a eukaryote cell has a double membrane and consists of chromosomes.

The endosymbionts also had only a single membrane. Mitochondria in eukaryotes, like the nucleus, have a double cell wall. As well, the endosymbionts closely resembled bacteria rather than mitochondria.

This last point is what makes the discovery of P. myojinensis so important.

There are two major theories about how eukaryotes evolved. The autogenesis theory proposes that a eukaryote’s structures developed from primitive prokaryotic features. The symbiogenesis theory – first properly described by Russian Konstantin Mereschkowski in 1910 and subsequently advanced by Lynn Margulis in 1967 – proposes that eukaryotes evolved from a symbiotic relationship after a bacteria was absorbed by larger achaean, eventually becoming an integral and working part of the cell.

P. myojinensis seems to be an organism that has incorporated endosymbionts into its structure but not yet developed the full range of eukaryotic functions.

As the authors of the paper suggest, “ … it may even be a conservative descendant of the transitional lineage between prokaryotes and eukaryotes.”

For a fuller description of the possible implications of the discovery, read this article on ABC online by British scientist Nick Lane, whose latest book The Vital Question: Why is life the way it is?, is a rewarding and thought-provoking read.